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Daniel Tranchina, Ph.D., B.A. - Publications

Affiliations: 
Mathematics, Biology, Center for Neuroscience New York University, New York, NY, United States 
Website:
http://biology.as.nyu.edu/object/DanielTranchina.html
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40/58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Athanasiadou R, Neymotin B, Brandt N, Wang W, Christiaen L, Gresham D, Tranchina D. A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory. Plos Computational Biology. 15: e1006794. PMID 30856174 DOI: 10.1371/Journal.Pcbi.1006794  0.348
2016 Warren TJ, Van Hook MJ, Tranchina D, Thoreson WB. Kinetics of Inhibitory Feedback from Horizontal Cells to Photoreceptors: Implications for an Ephaptic Mechanism. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 36: 10075-88. PMID 27683904 DOI: 10.1523/Jneurosci.1090-16.2016  0.351
2014 Steele SA, Tranchina D, Rinzel J. An alternating renewal process describes the buildup of perceptual segregation. Frontiers in Computational Neuroscience. 8: 166. PMID 25620927 DOI: 10.3389/Fncom.2014.00166  0.375
2014 Ekanadham C, Tranchina D, Simoncelli EP. A unified framework and method for automatic neural spike identification. Journal of Neuroscience Methods. 222: 47-55. PMID 24184059 DOI: 10.1016/J.Jneumeth.2013.10.001  0.348
2012 Chen CK, Woodruff ML, Chen FS, Chen Y, Cilluffo MC, Tranchina D, Fain GL. Modulation of mouse rod response decay by rhodopsin kinase and recoverin. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 32: 15998-6006. PMID 23136436 DOI: 10.1523/Jneurosci.1639-12.2012  0.3
2012 Stinchcombe AR, Peskin CS, Tranchina D. Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 061919. PMID 23005139 DOI: 10.1103/Physreve.85.061919  0.749
2011 Ekanadham C, Tranchina D, Simoncelli E. Recovery of sparse translation-invariant signals with continuous basis pursuit. Ieee Transactions On Signal Processing : a Publication of the Ieee Signal Processing Society. 59. PMID 24352562 DOI: 10.1109/Tsp.2011.2160058  0.306
2010 Tranchina D. Population Density Methods in Large-Scale Neural Network Modelling Stochastic Methods in Neuroscience. DOI: 10.1093/acprof:oso/9780199235070.003.0007  0.334
2009 Ly C, Tranchina D. Spike train statistics and dynamics with synaptic input from any renewal process: a population density approach. Neural Computation. 21: 360-96. PMID 19431264 DOI: 10.1162/Neco.2008.03-08-743  0.651
2008 Goodhill G, Baker C, Balasubramanian V, Bazhenov M, Beck J, Becker S, Bethge M, Boahen K, Boden M, Bonin V, Bouret S, Fairhall A, Flash T, French R, Gillies A, ... ... Tranchina D, et al. Network: Computation in Neural Systems: Editorial Network: Computation in Neural Systems. 19: 1-2. DOI: 10.1080/09548980801915409  0.318
2007 Ly C, Tranchina D. Critical analysis of dimension reduction by a moment closure method in a population density approach to neural network modeling. Neural Computation. 19: 2032-92. PMID 17571938 DOI: 10.1162/Neco.2007.19.8.2032  0.707
2006 Apfaltrer F, Ly C, Tranchina D. Population density methods for stochastic neurons with realistic synaptic kinetics: firing rate dynamics and fast computational methods. Network (Bristol, England). 17: 373-418. PMID 17162461 DOI: 10.1080/09548980601069787  0.649
2006 Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA synthesis in mammalian cells. Plos Biology. 4: e309. PMID 17048983 DOI: 10.1371/Journal.Pbio.0040309  0.312
2005 Cadetti L, Tranchina D, Thoreson WB. A comparison of release kinetics and glutamate receptor properties in shaping rod-cone differences in EPSC kinetics in the salamander retina. The Journal of Physiology. 569: 773-88. PMID 16223761 DOI: 10.1113/Jphysiol.2005.096545  0.437
2005 Hamer RD, Nicholas SC, Tranchina D, Lamb TD, Jarvinen JL. Toward a unified model of vertebrate rod phototransduction. Visual Neuroscience. 22: 417-36. PMID 16212700 DOI: 10.1017/S0952523805224045  0.338
2003 Thoreson WB, Tranchina D, Witkovsky P. Kinetics of synaptic transfer from rods and cones to horizontal cells in the salamander retina. Neuroscience. 122: 785-98. PMID 14622921 DOI: 10.1016/J.Neuroscience.2003.08.012  0.409
2003 Hamer RD, Nicholas SC, Tranchina D, Liebman PA, Lamb TD. Multiple steps of phosphorylation of activated rhodopsin can account for the reproducibility of vertebrate rod single-photon responses. The Journal of General Physiology. 122: 419-44. PMID 12975449 DOI: 10.1085/Jgp.200308832  0.326
2001 Hayot F, Tranchina D. Modeling corticofugal feedback and the sensitivity of lateral geniculate neurons to orientation discontinuity. Visual Neuroscience. 18: 865-77. PMID 12020077 DOI: 10.1017/S0952523801186037  0.476
2001 Witkovsky P, Thoreson W, Tranchina D. Transmission at the photoreceptor synapse. Progress in Brain Research. 131: 145-59. PMID 11420937 DOI: 10.1016/S0079-6123(01)31013-0  0.352
2001 Haskell E, Nykamp DQ, Tranchina D. Population density methods for large-scale modelling of neuronal networks with realistic synaptic kinetics: cutting the dimension down to size. Network (Bristol, England). 12: 141-74. PMID 11405420 DOI: 10.1080/Net.12.2.141.174  0.786
2001 Nykamp DQ, Tranchina D. A population density approach that facilitates large-scale modeling of neural networks: extension to slow inhibitory synapses. Neural Computation. 13: 511-46. PMID 11244554 DOI: 10.1162/089976601300014448  0.789
2001 Haskell E, Nykamp DQ, Tranchina D. A population density method for large-scale modeling of neuronal networks with realistic synaptic kinetics Neurocomputing. 38: 627-632. DOI: 10.1016/S0925-2312(01)00407-6  0.778
2000 Nykamp DQ, Tranchina D. A population density approach that facilitates large-scale modeling of neural networks: analysis and an application to orientation tuning. Journal of Computational Neuroscience. 8: 19-50. PMID 10798498 DOI: 10.1023/A:1008912914816  0.797
2000 Nykamp DQ, Tranchina D. Fast neural network simulations with population density methods Neurocomputing. 32: 487-492. DOI: 10.1016/S0925-2312(00)00203-4  0.777
1998 Surkis A, Peskin CS, Tranchina D, Leonard CS. Recovery of cable properties through active and passive modeling of subthreshold membrane responses from laterodorsal tegmental neurons. Journal of Neurophysiology. 80: 2593-607. PMID 9819266 DOI: 10.1152/Jn.1998.80.5.2593  0.392
1998 Tranchina D. The calculus of rod phototransduction. The Journal of General Physiology. 111: 3-6. PMID 9417131 DOI: 10.1085/Jgp.111.1.3  0.338
1997 Witkovsky P, Schmitz Y, Akopian A, Krizaj D, Tranchina D. Gain of rod to horizontal cell synaptic transfer: relation to glutamate release and a dihydropyridine-sensitive calcium current. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 17: 7297-306. PMID 9295376 DOI: 10.1523/Jneurosci.17-19-07297.1997  0.369
1995 Reifsnider ES, Tranchina D. Background contrast modulates kinetics and lateral spread of responses to superimposed stimuli in outer retina. Visual Neuroscience. 12: 1105-26. PMID 8962830 DOI: 10.1017/S0952523800006751  0.437
1994 Cadenas ID, Reifsnider ES, Tranchina D. Modulation of synaptic transfer between retinal cones and horizontal cells by spatial contrast. The Journal of General Physiology. 104: 567-91. PMID 7807061 DOI: 10.1085/Jgp.104.3.567  0.384
1992 Golard A, Witkovsky P, Tranchina D. Membrane currents of horizontal cells isolated from turtle retina. Journal of Neurophysiology. 68: 351-61. PMID 1382117 DOI: 10.1152/Jn.1992.68.2.351  0.31
1991 Tranchina D, Sneyd J, Cadenas ID. Light adaptation in turtle cones. Testing and analysis of a model for phototransduction. Biophysical Journal. 60: 217-37. PMID 1653050 DOI: 10.1016/S0006-3495(91)82045-8  0.307
1990 Purpura K, Tranchina D, Kaplan E, Shapley RM. Light adaptation in the primate retina: analysis of changes in gain and dynamics of monkey retinal ganglion cells. Visual Neuroscience. 4: 75-93. PMID 2176096 DOI: 10.1017/S0952523800002789  0.713
1989 Sneyd J, Tranchina D. Phototransduction in cones: an inverse problem in enzyme kinetics. Bulletin of Mathematical Biology. 51: 749-84. PMID 2573396 DOI: 10.1007/Bf02459659  0.385
1989 Witkovsky P, Stone S, Tranchina D. Photoreceptor to horizontal cell synaptic transfer in the Xenopus retina: modulation by dopamine ligands and a circuit model for interactions of rod and cone inputs. Journal of Neurophysiology. 62: 864-81. PMID 2530319 DOI: 10.1152/Jn.1989.62.4.864  0.367
1988 Tranchina D, Peskin CS. Light adaptation in the turtle retina: embedding a parametric family of linear models in a single nonlinear model. Visual Neuroscience. 1: 339-48. PMID 3154803 DOI: 10.1017/S0952523800004119  0.34
1986 Tranchina D, Nicholson C. A model for the polarization of neurons by extrinsically applied electric fields. Biophysical Journal. 50: 1139-56. PMID 3801574 DOI: 10.1016/S0006-3495(86)83558-5  0.35
1984 Dawis S, Shapley R, Kaplan E, Tranchina D. The receptive field organization of X-cells in the cat: spatiotemporal coupling and asymmetry. Vision Research. 24: 549-64. PMID 6740975 DOI: 10.1016/0042-6989(84)90109-3  0.537
1984 Tranchina D, Gordon J, Shapley RM. Retinal light adaptation--evidence for a feedback mechanism. Nature. 310: 314-6. PMID 6462216 DOI: 10.1038/310314A0  0.573
1983 Tranchina D, Gordon J, Shapley R. Spatial and temporal properties of luminosity horizontal cells in the turtle retina. The Journal of General Physiology. 82: 573-98. PMID 6644270 DOI: 10.1085/Jgp.82.5.573  0.54
1981 Tranchina D, Gordon J, Shapley R, Toyoda J. Linear information processing in the retina: a study of horizontal cell responses. Proceedings of the National Academy of Sciences of the United States of America. 78: 6540-2. PMID 6947242 DOI: 10.1073/Pnas.78.10.6540  0.533
Low-probability matches (unlikely to be authored by this person)
1994 Okada YC, Huang JC, Rice ME, Tranchina D, Nicholson C. Origin of the apparent tissue conductivity in the molecular and granular layers of the in vitro turtle cerebellum and the interpretation of current source-density analysis. Journal of Neurophysiology. 72: 742-53. PMID 7983532 DOI: 10.1152/Jn.1994.72.2.742  0.288
2010 Chen J, Woodruff ML, Wang T, Concepcion FA, Tranchina D, Fain GL. Channel modulation and the mechanism of light adaptation in mouse rods. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 30: 16232-40. PMID 21123569 DOI: 10.1523/Jneurosci.2868-10.2010  0.26
1984 Peskin CS, Tranchina D, Hull DM. How to see in the dark: photon noise in vision and nuclear medicine. Annals of the New York Academy of Sciences. 435: 48-72. PMID 6598007 DOI: 10.1111/J.1749-6632.1984.Tb13740.X  0.256
2011 Ekanadham C, Tranchina D, Simoncelli EP. A blind deconvolution method for neural spike identification Advances in Neural Information Processing Systems 24: 25th Annual Conference On Neural Information Processing Systems 2011, Nips 2011.  0.244
2009 Nero D, Katari MS, Kelfer J, Tranchina D, Coruzzi GM. In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana. Bmc Bioinformatics. 10: 435. PMID 20025756 DOI: 10.1186/1471-2105-10-435  0.242
2002 Hamer RD, Nicholas SC, Tranchina D, Liebman PA. On the reproducibility of single photon responses (SRPs): The gordian knot of rod phototransduction perseveres Journal of Vision. 2: 113a. DOI: 10.1167/2.10.113  0.238
2013 Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD. Plasticity regulators modulate specific root traits in discrete nitrogen environments. Plos Genetics. 9: e1003760. PMID 24039603 DOI: 10.1371/Journal.Pgen.1003760  0.234
2009 Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutiérrez RA. A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. Plos Computational Biology. 5: e1000326. PMID 19300494 DOI: 10.1371/Journal.Pcbi.1000326  0.227
2009 Nero D, Krouk G, Tranchina D, Coruzzi GM. A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule". Bmc Systems Biology. 3: 59. PMID 19500399 DOI: 10.1186/1752-0509-3-59  0.226
2019 Swift J, Adame M, Tranchina D, Henry A, Coruzzi GM. Water impacts nutrient dose responses genome-wide to affect crop production. Nature Communications. 10: 1374. PMID 30914651 DOI: 10.1038/S41467-019-09287-7  0.211
2002 Lee SS, Tranchina D, Ohta Y, Flajnik MF, Hsu E. Hypermutation in shark immunoglobulin light chain genes results in contiguous substitutions. Immunity. 16: 571-82. PMID 11970880 DOI: 10.1016/S1074-7613(02)00300-X  0.206
2021 Abdul-Rahman F, Tranchina D, Gresham D. Fluctuating environments maintain genetic diversity through neutral fitness effects and balancing selection. Molecular Biology and Evolution. PMID 34132791 DOI: 10.1093/molbev/msab173  0.149
1987 Peskin CS, McQueen DM, Fogelson AL, Tranchina D, Lacker HM, Novick RP. MATHEMATICAL MODELS IN PHYSIOLOGY Ieee/Engineering in Medicine and Biology Society Annual Conference. 1120-1122.  0.103
2023 Sun S, Tranchina D, Gresham D. Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence. Biorxiv : the Preprint Server For Biology. PMID 37577636 DOI: 10.1101/2023.08.03.551843  0.094
1976 Starzak ME, Tranchina DA. An open system kinetic transport model for the Hodgkin-Huxley equations. Journal of Theoretical Biology. 56: 283-99. PMID 1271823 DOI: 10.1016/S0022-5193(76)80076-8  0.089
2023 Plavskin Y, de Biase MS, Ziv N, Janská L, Zhu YO, Hall DW, Schwarz RF, Tranchina D, Siegal M. Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects. Biorxiv : the Preprint Server For Biology. PMID 37461506 DOI: 10.1101/2023.07.04.547687  0.078
1996 Tranchina D. Phototransduction in rods: A theoretical analysis of inactivation kinetics, saturation and noise Investigative Ophthalmology and Visual Science. 37: S811.  0.063
2011 Ekanadham C, Tranchina D, Simoncelli EP. Sparse decomposition of transformation-invariant signals with continuous basis pursuit Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. DOI: 10.1109/ICASSP.2011.5947244  0.062
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